CD-CODE API issueshttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues2022-09-28T09:24:36Zhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/36"pubmed_ids" is null2022-09-28T09:24:36Zmoon"pubmed_ids" is nullhttps://cd-code.org/condensate/hybrid_D0PV95_C5MKY7_X5DSL3 gives pubmed_ids well.
![1](/uploads/4d05b4ada257131a4fde67bb4cf788b3/1.png)
Strangely, in Dev, https://dev.cd-code.org/condensate/hybrid_D0PV95_C5MKY7_X5DSL3 does not have it.
...https://cd-code.org/condensate/hybrid_D0PV95_C5MKY7_X5DSL3 gives pubmed_ids well.
![1](/uploads/4d05b4ada257131a4fde67bb4cf788b3/1.png)
Strangely, in Dev, https://dev.cd-code.org/condensate/hybrid_D0PV95_C5MKY7_X5DSL3 does not have it.
![2](/uploads/b7ac7231e7e2d3fe72149d8cd588d7e1/2.png)sghoshsghoshhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/35New attributes to be opened2022-09-05T09:10:33ZsghoshNew attributes to be opened1. Protein Detail > condensates > protein_functional_type
2. Protein List > biomolecular_condensate_count1. Protein Detail > condensates > protein_functional_type
2. Protein List > biomolecular_condensate_countsghoshsghoshhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/34Antibody Link doesnt exists for many proteins2022-09-05T09:23:58ZsghoshAntibody Link doesnt exists for many proteinsFor many proteins, there is no corresponding page in Protein Atlas. Have to check this
**Example:**
https://cd-code.org/protein/Q7T226
=>
https://www.proteinatlas.org/Q7T226-unknown/antibody
https://cd-code.org/protein/Q5A8T7
=>
http...For many proteins, there is no corresponding page in Protein Atlas. Have to check this
**Example:**
https://cd-code.org/protein/Q7T226
=>
https://www.proteinatlas.org/Q7T226-unknown/antibody
https://cd-code.org/protein/Q5A8T7
=>
https://www.proteinatlas.org/Q5A8T7-unknown/antibodyhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/33API Key Generator2022-09-14T11:38:37ZsghoshAPI Key GeneratorA CMD utility to generate API Key on demand against some ID of the client and store it in a database for auditability.A CMD utility to generate API Key on demand against some ID of the client and store it in a database for auditability.https://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/32Generate API Documentation for direct use2022-07-21T11:30:54ZsghoshGenerate API Documentation for direct useSomething like swaggerSomething like swaggersghoshsghoshhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/31functional type field is missing in the protein table in CondensateDetailPage2022-05-02T10:52:43Zmoonfunctional type field is missing in the protein table in CondensateDetailPagefunctional type exists but this value is not collected in condensate data.
E.g. https://dev.ddcode.org/condensate/nucleolus__3702
![1](/uploads/022362d1259bed04d41bd021884452bc/1.png)
![2](/uploads/a180124a4a3572aa0c9aa2de34a2bf8d/2.pn...functional type exists but this value is not collected in condensate data.
E.g. https://dev.ddcode.org/condensate/nucleolus__3702
![1](/uploads/022362d1259bed04d41bd021884452bc/1.png)
![2](/uploads/a180124a4a3572aa0c9aa2de34a2bf8d/2.png)
Also there is a strange string e.g. random_id in pubmed array.sghoshsghoshhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/30New condensate-specific protein attributes2022-05-04T04:34:22ZsghoshNew condensate-specific protein attributes```
**New attributes for a condensate:**
1. protein_functional_type: dict
Key: Protein's Uniprot ID
Value: functional type in this condensate ("driver"/"client"/"regulator")
2. protein_driver_criterion: dict
Key: Protein's Uniprot ID
V...```
**New attributes for a condensate:**
1. protein_functional_type: dict
Key: Protein's Uniprot ID
Value: functional type in this condensate ("driver"/"client"/"regulator")
2. protein_driver_criterion: dict
Key: Protein's Uniprot ID
Value: criterion fulfilled to qualify as a driver ("self_ps", "induce_formation", "intergrity_essential")
3. protein_exp_evidence: dict
Key: Protein's Uniprot ID
Value: experimental evidence ("in_vivo", "in_vitro", "in_tergrity_essential_cellulo")
```sghoshsghoshhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/29Logger2022-04-05T09:01:35ZsghoshLoggersghoshsghoshhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/27API Key for authentication2022-02-18T13:12:22ZsghoshAPI Key for authenticationAPI_KEY read from env variable.
To generate an API_KEY, one can use `secrets.token_urlsafe(16)`
https://docs.python.org/3/library/secrets.htmlAPI_KEY read from env variable.
To generate an API_KEY, one can use `secrets.token_urlsafe(16)`
https://docs.python.org/3/library/secrets.htmlsghoshsghoshhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/26Expose new fields2021-11-04T16:33:04ZsghoshExpose new fields**Proteins**
- source_db_tags
- pubmed_ids
**Condensates**
- protein_source_db_tags
- protein_pubmed_ids**Proteins**
- source_db_tags
- pubmed_ids
**Condensates**
- protein_source_db_tags
- protein_pubmed_idssghoshsghoshhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/25LLPS PTMs not showing up2021-11-02T14:46:58ZsghoshLLPS PTMs not showing upProtein `P22626-2` not showing `llps_ptms`Protein `P22626-2` not showing `llps_ptms`sghoshsghoshhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/24Inconsistent array order for protein_evidence_map2021-06-16T13:59:26ZmoonInconsistent array order for protein_evidence_mapI noticed that there are inconsistent order in evidence map item.
![1](/uploads/c0b03d5832cec4bbc7d136981da4f2a5/1.png)
You can find it in http://ddcode-dev.mpi-cbg.de/api/condensates/nucleolus__9606I noticed that there are inconsistent order in evidence map item.
![1](/uploads/c0b03d5832cec4bbc7d136981da4f2a5/1.png)
You can find it in http://ddcode-dev.mpi-cbg.de/api/condensates/nucleolus__9606sghoshsghoshhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/23CI/CD setup for Dev API server2021-06-09T10:31:32ZsghoshCI/CD setup for Dev API serverI was wondering if a continuous development setup is possible for the `dev/test` version for the API service. Something like whenever I make a push to the `development` branch, the same is pulled on the server and the service is restarte...I was wondering if a continuous development setup is possible for the `dev/test` version for the API service. Something like whenever I make a push to the `development` branch, the same is pulled on the server and the service is restarted.
I know this is possible with Jenkins, and there is an option to integrate that easily on Gitlab. @moon can you check this and configure this. This will help me in end-to-end testing while any incremental changes I make to the API codebase.moonsghoshmoonhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/22CI/CD setup for Dev API server2024-02-29T19:55:40ZsghoshCI/CD setup for Dev API serverI was wondering if a continuous development setup is possible for the `dev/test` version for the API service. Something like whenever I make a push to the `development` branch, the same is pulled on the server and the service is restarte...I was wondering if a continuous development setup is possible for the `dev/test` version for the API service. Something like whenever I make a push to the `development` branch, the same is pulled on the server and the service is restarted.
I know this is possible with Jenkins, and there is an option to integrate that easily on Gitlab. @moon can you check this and configure this. This will help me in end-to-end testing while any incremental changes I make to the API codebase.moonsghoshmoonhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/21Query Param in List API for specific fields projection2021-07-16T09:58:46ZsghoshQuery Param in List API for specific fields projectionNew query parameter `fields` takes a comma-separated list of attributes of the entity in the list APIs.New query parameter `fields` takes a comma-separated list of attributes of the entity in the list APIs.sghoshsghoshhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/20wiki interface2021-06-03T11:29:45Zmoonwiki interfaceIn demo version, there is wiki api interface which should be implemented in dev version too.
Please check the PR !1.In demo version, there is wiki api interface which should be implemented in dev version too.
Please check the PR !1.sghoshsghoshhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/19Condensates list for Chimera (species == null)2021-06-02T09:21:55ZmoonCondensates list for Chimera (species == null)There is no way to get the list of Chimera condensates as Chimera's species is null in this case. Demo api accepts ```/condensates?species_tax_id=null``` for it.
It is also a good idea to have ```/condensates?species_tax_id=all``` for li...There is no way to get the list of Chimera condensates as Chimera's species is null in this case. Demo api accepts ```/condensates?species_tax_id=null``` for it.
It is also a good idea to have ```/condensates?species_tax_id=all``` for listing condensates of all the species except Chimera.sghoshsghoshhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/18/species [GET] does not return all the species2021-06-22T15:27:42Zmoon/species [GET] does not return all the speciesThe below codes does not return the same results of http://ddcode-srv1:5001/species.
```python
@app.route('/species', methods=['GET'])
def species_list():
response = {
'data': statistics.get_species_wise_condensates()
}
...The below codes does not return the same results of http://ddcode-srv1:5001/species.
```python
@app.route('/species', methods=['GET'])
def species_list():
response = {
'data': statistics.get_species_wise_condensates()
}
return jsonify(response)
```
The error codes:
```bash
[2021-05-27 16:18:25,573] ERROR in app: Exception on /species [GET]
Traceback (most recent call last):
File "/Users/moon/Projects/gitlab/dd-code/dev/dd-code-api/dd_venv/lib/python3.9/site-packages/flask/app.py", line 2070, in wsgi_app
response = self.full_dispatch_request()
File "/Users/moon/Projects/gitlab/dd-code/dev/dd-code-api/dd_venv/lib/python3.9/site-packages/flask/app.py", line 1515, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/Users/moon/Projects/gitlab/dd-code/dev/dd-code-api/dd_venv/lib/python3.9/site-packages/flask/app.py", line 1513, in full_dispatch_request
rv = self.dispatch_request()
File "/Users/moon/Projects/gitlab/dd-code/dev/dd-code-api/dd_venv/lib/python3.9/site-packages/flask/app.py", line 1499, in dispatch_request
return self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args)
File "/Users/moon/Projects/gitlab/dd-code/dev/dd-code-api/app.py", line 37, in species_list
'data': statistics.get_species_wise_condensates()
AttributeError: 'function' object has no attribute 'get_species_wise_condensates'
127.0.0.1 - - [27/May/2021 16:18:25] "GET /species HTTP/1.1" 500 -
```sghoshsghoshhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/17Flask app requires CORS wrapper for access to API2021-06-02T09:21:24ZmoonFlask app requires CORS wrapper for access to APIFlask app needs CORS wrapper in order to access from the front-end web browser.
![1](/uploads/a7679c497a8e270d01b1c14bb74ac024/1.png)Flask app needs CORS wrapper in order to access from the front-end web browser.
![1](/uploads/a7679c497a8e270d01b1c14bb74ac024/1.png)sghoshsghoshhttps://git.mpi-cbg.de/dd-code-team/dd-code-api/-/issues/16Remove "Browse" Page; Replace with example page2021-05-27T08:26:09ZsghoshRemove "Browse" Page; Replace with example page1. Remove the Browse Page, this won't be so useful once we have the separate listing page for "Biomolecular Condensates"
2. New tabs for Example pages - one for condensate and one for protein (Willis or Agnes to say which specific example)1. Remove the Browse Page, this won't be so useful once we have the separate listing page for "Biomolecular Condensates"
2. New tabs for Example pages - one for condensate and one for protein (Willis or Agnes to say which specific example)moonmoon